A second-half Emmanuel Emenike strike looked to have been enough to hand Nigeria a vital three points and leave the Chipolopolo on the brink of a shock first-round exit.
But Mweene’s ice-cool spot-kick five minutes from time means the spoils were shared, with the group door left ajar for Burkina Faso and Ethiopia who play later on Friday night.
The game could have been out of reach by that stage for Zambia, but Chelsea star John Obi Mikel missed a first half penalty.
Neither side had an opening 45 minutes to remember on a sandy pitch at the Mbombela Stadium in Nelspruit, with the best chance falling to Nigeria captain Mikel, who fluffed his lines from 12 yards.
Nigeria, who shaded the possession at the break, were awarded the spot-kick after Davies Nkausu up-ended Ahmed Musa on the corner of the box.
But Mikel, who has scored just once since 2008, hit a tame penalty against the outside of the post.
Chisamba Lungu went closest for the reigning champions in the opening 45 minutes, but his curling free-kick was turned around the near post by Vincent Enyeama at ful-stretch.
It was Eminike who made the breakthrough 11 minutes after the break, as the Spartak Moscow striker powered home a shot from the edge of the box to tip the game in the Super Eagles’ favour.
Zambia really should have been level on 72 minutes but Rainford Kalaba fired his shot straight at Enyeama after working his way into the box neatly.
Substitute Collins Mbesuma had an even better chance to draw the Chipolopolo but fired wide after a superb cut-back from Kalaba.
And it was Hervé Renard’s side who had the last word after referee Grisha Ghead adjudged Lazio midfield Ogenyi Onazi to have fouled Emmanuel Mayaka on the edge of the box.
Mweene made no mistake from the spot, but both sides know they will have to play better if they are to have any chance to progressing.
Get enhanced odds of 7/1 on Rangers to get promoted on Thursday with Paddy Power.